› 1f7u

X-ray diffraction
2.2Å resolution

CRYSTAL STRUCTURE OF THE ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNA(ARG) AND L-ARG

Released:
DOI: 10.2210/pdb1f7u/pdb
PDB entry 1f7u coloured by chain, front view.
PDB entry 1f7u coloured by chain, side view.
PDB entry 1f7u coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding.
Delagoutte B, Moras D, Cavarelli J
EMBO J 19 5599-610 (2000)
PMID: 11060012

Function and Biology Details

Reaction catalysed: 
ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170210 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Arginine--tRNA ligase, cytoplasmic Chain: A
Molecule details ›
Chain: A
Length: 607 amino acids
Theoretical weight: 69.62 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q05506 (Residues: 1-607; Coverage: 100%)
Gene names: D9651.10, YDR341C
Sequence domains:
Structure domains:
TRNA(ARG) Chain: B
Molecule details ›
Chain: B
Length: 76 nucleotides
Theoretical weight: 24.57 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand ARG 1 x ARG
8 modified residues:
Ligand PSU 3 x PSU
Ligand 1MG 1 x 1MG
Ligand 2MG 1 x 2MG
Ligand H2U 3 x H2U
Ligand M2G 1 x M2G
Ligand 5MC 1 x 5MC
Ligand 5MU 1 x 5MU
Ligand 1MA 1 x 1MA

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21212
Unit cell:
a: 129.646Å b: 107.472Å c: 71.379Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.19 0.233
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity.
Agris et al. (2017)
10 more

35 mentions without citation

Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs.
Tragni et al. (2022)
34 more